Publications (20)
PRIMAD-LID: A Developed Framework for Computational Reproducibility
Meznah Aloqalaa, Stian Soiland-Reyes, Carole Goble
Over the past decade alongside increased focus on computational reproducibility significant efforts have been made to define reproducibility. However, these definitions provide a t…
One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project
Frank T. Bergmann, Richard Adams, Stuart Moodie +15
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily…
Workflows Community Summit 2022: A Roadmap Revolution
Rafael Ferreira da Silva, Rosa M. Badia, Venkat Bala +102
Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex s…
Recording provenance of workflow runs with RO-Crate
Simone Leo, Michael R. Crusoe, Laura RodrÃguez-Navas +15
Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have…
WorkflowHub: a registry for computational workflows
Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall +12
The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both…
Systematically Examining Reproducibility: A Case Study for High Throughput Sequencing using the PRIMAD Model and BioCompute Object
Meznah Aloqalaa, Stian Soiland-Reyes, Carole Goble
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generati…
The Archive and Package (arcp) URI scheme
Stian Soiland-Reyes, Marcos Cáceres
The arcp URI scheme is introduced for location-independent identifiers to consume or reference hypermedia and linked data resources bundled inside a file archive, as well as to res…
Packaging research artefacts with RO-Crate
Stian Soiland-Reyes, Peter Sefton, Mercè Crosas +13
An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific a…
Web Annotation as a First Class Object
Paolo Ciccarese, Stian Soiland-Reyes, Tim Clark
Scholars have made handwritten notes and comments in books and manuscripts for centuries. Today's blogs and news sites typically invite users to express their opinions on the publi…
Evaluating FAIR Digital Object and Linked Data as distributed object systems
Stian Soiland-Reyes, Carole Goble, Paul Groth
FAIR Digital Object (FDO) is an emerging concept that is highlighted by European Open Science Cloud (EOSC) as a potential candidate for building a ecosystem of machine-actionable r…
PAV ontology: Provenance, Authoring and Versioning
Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame +3
Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-rev…
An Ecosystem of Services for FAIR Computational Workflows
Sean R. Wilkinson, Johan Gustafsson, Finn Bacall +22
Computational workflows represent major investments of effort and expertise. As first-class, publishable research objects of their own, they are key to sharing methodological know-…
Applying the FAIR Principles to computational workflows
Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame +20
Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also…
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup +7
Computational Workflows are widely used in data analysis, enabling innovation and decision-making. In many domains (bioinformatics, image analysis, & radio astronomy) the analysis…
A Community Roadmap for Scientific Workflows Research and Development
Rafael Ferreira da Silva, Henri Casanova, Kyle Chard +26
The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a…
The role of metadata in reproducible computational research
Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt +3
Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In additio…
Structuring research methods and data with the Research Object model: genomics workflows as a case study
Kristina M. Hettne, Harish Dharuri, Jun Zhao +16
One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand mol…
Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows
Rafael Ferreira da Silva, Deborah Bard, Kyle Chard +108
The Workflows Community Summit gathered 111 participants from 18 countries to discuss emerging trends and challenges in scientific workflows, focusing on six key areas: time-sensit…
Taverna Mobile: Taverna workflows on Android
Hyde Zhang, Stian Soiland-Reyes, Carole Goble
Researchers are often on the move, say at conferences or projects meetings, and as workflows are becoming ubiquitous in the scientific process, having access to scientific workflow…
Workflows Community Summit: Bringing the Scientific Workflows Community Together
Rafael Ferreira da Silva, Henri Casanova, Kyle Chard +42
Scientific workflows have been used almost universally across scientific domains, and have underpinned some of the most significant discoveries of the past several decades. Many of…